Metroid Prime Trilogy contains 1 Wii game (MP3) and 2 GC games (MP1 &MP2). Since MP1 and MP2 are actualy gamecube games Im wondering if it is possible to replace the MP1/MP2 partitions with a gamecube Iso so that you can play a gc game with a USB Loader in Wii mode. This might be a stupid idea but who knows

Sorry to bust your bubble, but that won't work. These games are ported to the wii and not run trough any emulator. Same goes for all the "New Control"-games and Resident Evil re-releases.
Why the hell would you think to emulate games that run natively in GC-mode on the Wii anyway?
Get a modchip instead, the solderless ones are not that expensive and you can runn all the GC games you want.

Metroid Prime Trilogy contains 1 Wii game (MP3) and 2 GC games (MP1 &MP2). Since MP1 and MP2 are actualy gamecube games Im wondering if it is possible to replace the MP1/MP2 partitions with a gamecube Iso so that you can play a gc game with a USB Loader in Wii mode. This might be a stupid idea but who knows

You do realise that it probably wont hurt to try replacing the partitions and shove it on a USB loader. The controls are probably hardcoded into the game partition and therefore if you put a GC game in it it will automatically use the GC controls.

Admittedly, I dont know much about how the wii works, but I think the games are just ports and not re-makes therefore it can't hurt to try. At most you will waste an hour or so of your time. If someone tried this and it did work, I'm sure it would be all over the forums, so it doesn't look like someone has tried (and succedded).

Just jump in there, and tell us what happens. I would, but I don't have access to a backup of MP3.